Return a cloned object from config.get()

This prevents mutations to the values of the default settings.

src/app/config.coffee

@@ -106,8 +106,8 @@ class Config
   # Returns the value from Atom's default settings, the user's configuration file,
   # or `null` if the key doesn't exist in either.
   get: (keyPath) ->
-    _.valueForKeyPath(@settings, keyPath) ?
-      _.valueForKeyPath(@defaultSettings, keyPath)
+    value = _.valueForKeyPath(@settings, keyPath) ? _.valueForKeyPath(@defaultSettings, keyPath)
+    _.deepClone(value)
 
   # Retrieves the setting for the given key as an integer.
   #

src/app/package-config-panel.coffee

@@ -29,11 +29,12 @@ class PackageConfigPanel extends ConfigPanel
     @on 'change', '#packages input[type=checkbox]', (e) ->
       checkbox = $(e.target)
       name = checkbox.closest('tr').attr('name')
+      disabledPackages = config.get('core.disabledPackages')
       if checkbox.attr('checked')
-        _.remove(config.get('core.disabledPackages'), name)
+        _.remove(disabledPackages, name)
       else
-        config.get('core.disabledPackages').push(name)
-      config.update()
+        disabledPackages.push(name)
+      config.set('core.disabledPackages', disabledPackages)
 
     @observeConfig 'core.disabledPackages', (disabledPackages) =>
       @packageTableBody.find("input[type='checkbox']").attr('checked', true)